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Bcbio-nextgen tutorial » History » Version 8

Bryan Cosca, 03/16/2015 07:03 PM

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h1. Running bcbio-nextgen using Arvados
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WIP
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h2. Uploading data through the web and using it on Arvados
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# In your home project, click on the blue *+ Add data* button in the top right.
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# Click *Upload files from my computer*
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# Click *Choose Files* and choose the 2 paired end fastq files you would like to run bcbio-nextgen on.
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# Once you're ready, click *> Start*
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# Feel free to rename your Collection so you can remember it later. Click on the pencil icon in the top left corner next to *New collection*
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# Once that is uploaded, navigate back to the dashboard and click on *Run a pipeline...* and choose bcbio-nextgen pipeline.
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# You can change the input by clicking on the *[Choose]* button next to the *R1 parameter* and *R2 parameter*.
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# Input your left fastq file as R1 and your right fastq file as R2.
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# For each fastq file, click on the dropdown menu, click on your newly-created project, and choose your desired input collection. 
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# Click *Run* to run bcbio on your data!
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h2. Uploading data through your shell and using it on Arvados
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Full documentation can be found "here":http://doc.arvados.org/user/tutorials/tutorial-keep.html
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# Install the "Arvados Python SDK":http://doc.arvados.org/sdk/python/sdk-python.html on the system from which you will upload the data (such as your workstation, or a server containing data from your sequencer). Doing so will install the Arvados file upload tool, arv-put.
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# To configure the environment with the Arvados instance host name and authentication token, see "here":http://doc.arvados.org/user/reference/api-tokens.html 
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# Navigate back to your Workbench dashboard and create a new project by clicking on the Projects dropdown menu and clicking Home. 
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# Click on [+ Add a subproject]. Feel free to edit the Project name or description by clicking the pencil to the right of the text.
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# To add data, return to your shell, create a folder, and put the two paired-end fastq files you want to upload inside. Use the command arv-put * --project-uuid qr1hi-xxxxx-yyyyyyyyyyyyyyy. The qr1hi tag can be found in the url of your new project. This ensures that all the files you would like to upload are in one collection.
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# The output value xxxxxxxxxxxxxxxxxxxx+yyyy is the Arvados collection locator that uniquely describes this file.
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# Once that is uploaded, navigate back to the dashboard and click on *Run a pipeline...* and choose bcbio-nextgen pipeline.
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# You can change the input by clicking on the *[Choose]* button next to the *R1 parameter* and *R2 parameter*.
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# Input your left fastq file as R1 and your right fastq file as R2.
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# For each fastq file, click on the dropdown menu, click on your newly-created project, and choose your desired input collection. 
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# Click *Run* to run bcbio on your data!
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h3. FAQ
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WIP